feat: update research skills part 7

[sixiang-svg]

New Skill Contribution

Skill Info

• Skill ID:
• Category:
• Description:

Checklist

• SKILL.md has valid YAML frontmatter with all required fields
• Skill ID matches the directory name
• Category is one of: productivity, development, communication, writing, research, other
• Instructions are clear and self-contained
• Instructions are under 4000 tokens
• No external URLs referenced in instructions
• Tested the skill with an AI agent and it produces good results
• Added usage examples in the frontmatter

Testing

Describe how you tested this skill:

Notes

Any additional context or notes for reviewers.

[greptile-apps]

Greptile Summary

This PR continues the "research skills update" series, applying a consistent structural template across 20 skills: enriching frontmatter with requires, examples, and improved description fields, and adding standardized ## Instruction, ## When to Use, and ## Output sections while stripping out code examples and external URL references.

Key observations:

• Positive: The new Instruction, When to Use, and Output sections are consistently well-written and specific to each skill's domain — a meaningful improvement over the prior placeholder content ("You need help with X.").
• pubmed-database/SKILL.md: The updated description now specifically claims PubMed search/retrieval, but the skill body covers the entire Biopython library (BLAST, phylogenetics, structural bioinformatics, etc.). Additionally, removal of code blocks left dangling headings with no content in the Installation, Common Patterns, and Writing Code sections, giving an AI agent incomplete instructions.
• pylabrobot/SKILL.md: The ## Instruction block was appended at the very end of the file rather than near the top, inconsistent with all other skills in this batch.
• qms-audit-expert/SKILL.md: The ## Resources section was removed, but the body text at lines 78 and 152–154 still contains Follow scripts/audit-prep-checklist.py and Follow references/regulatory-inspection-guide.md etc., creating stale, unresolvable references for agents.
• 13 files are missing a trailing newline (pycse, pylabrobot, pymatgen, pyopenms, pythia-event-generator, qlm-calibration, radio-copilot, rag-implementation, rdkit, research-engineer, research-grants, research-lookup, safety-system-skill).

Confidence Score: 3/5

• Mostly safe to merge, but pubmed-database and qms-audit-expert have quality issues that could mislead AI agents using those skills.
• The majority of the 20 skills receive clean, meaningful improvements. However, pubmed-database has a description-content mismatch and multiple empty sections that leave an agent without actionable guidance. The qms-audit-expert retains stale body references to deleted resource files. The pylabrobot Instruction placement is structurally inconsistent. The widespread missing newlines (13 files) are minor but reflect a templating gap in the PR's generation process.
• Pay close attention to skills/Research/pubmed-database/SKILL.md (description mismatch + empty sections) and skills/Research/qms-audit-expert/SKILL.md (stale file references in body text).

Important Files Changed

Filename	Overview
skills/Research/pubmed-database/SKILL.md	Description updated to be PubMed-specific but content covers full Biopython library; code block removal left orphaned headings with no body in Installation, Common Patterns, and Writing Code sections.
skills/Research/pylabrobot/SKILL.md	Frontmatter enriched; Instruction section added but placed at end of file (after Common Workflows) instead of near the top like all other skills; missing trailing newline.
skills/Research/pyopenms/SKILL.md	Code blocks removed; installation section now reads "Install using uv" and "Verify installation" as plain sentences (no code), leaving actionable guidance incomplete; missing trailing newline.
skills/Research/pysam/SKILL.md	Code blocks removed from Quick Start; section headers like "Read alignment file:" remain but their code bodies were removed, leaving empty example stubs.
skills/Research/pytdc/SKILL.md	Large cleanup removing code blocks; inline reference to removed files (references/oracles.md, scripts/molecular_generation.py) still exists in body text at line 160.
skills/Research/qms-audit-expert/SKILL.md	Resources section removed but body text retains stale references to scripts/audit-prep-checklist.py and references/regulatory-inspection-guide.md at lines 78 and 152–154.
skills/Research/qutip/SKILL.md	Code blocks removed from all workflow examples; section headers like "Simulating a Damped Harmonic Oscillator" now have empty bodies, but the Instruction/When to Use/Output blocks are well-formed.
skills/Research/research-engineer/SKILL.md	Large reduction removing code examples and reference tables; dependencies field dropped and replaced with requires: []; missing trailing newline (previously flagged in earlier review).
skills/Research/scanpy/SKILL.md	Large removal of code examples from all workflow sections; Instruction/Output blocks added; id/name still say "scanpy" despite content being about CZ CELLxGENE Census (pre-existing mismatch, not introduced by this PR).

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A[Skill YAML Frontmatter] --> B[id / name / description]
    A --> C[category: Research]
    A --> D[requires: empty list]
    A --> E[examples: 2 usage prompts]

    F[Skill Body Content] --> G[## Instruction\nStep-by-step agent directives]
    F --> H[## When to Use\nTrigger conditions]
    F --> I[## Output\nExpected deliverables]
    F --> J[Domain Reference Sections\nCapabilities / Workflows / etc.]

    G --> K{Code Examples\nPresent?}
    K -- Yes --> L[Retained\ne.g. pysam, qms-audit-expert]
    K -- No --> M[Removed\ne.g. pubmed-database, qutip, pylabrobot]

    M --> N{Orphaned\nSection Headings?}
    N -- Yes --> O[⚠️ Issue: Empty body\npubmed-database, pyopenms]
    N -- No --> P[✅ Clean removal]

    style O fill:#ffcccc,stroke:#cc0000
    style P fill:#ccffcc,stroke:#009900

Loading

Comments Outside Diff (2)

1. skills/Research/pubmed-database/SKILL.md, line 47-54 (link)

   Orphaned section headings with empty bodies after code removal

   The "Installation and Setup" section ends with two dangling sentences that previously led directly into code blocks, but the blocks were removed without any prose replacement:

   • Line 49: "Install Biopython using pip (requires Python 3 and NumPy):" — followed by nothing
   • Line 51: "For NCBI database access, always set your email address (required by NCBI):" — followed by a blank line

   An agent reading this section gets incomplete instructions. Similarly, the "Writing Biopython Code" section (lines 140–154) lists six numbered principles that each end with a colon or period but have no supporting examples or code, and the "Common Patterns" section (lines 156–165) names four workflow patterns (e.g., "Pattern 1: Fetch Sequence from GenBank") with completely empty bodies. Either restore concise code snippets, add a prose description, or remove the empty headings to avoid misleading users.

2. skills/Research/qms-audit-expert/SKILL.md, line 78 (link)

   Body text still references removed script and reference files

   This PR removed the entire ## Resources section that listed scripts and reference files. However, the body of the skill still contains inline references to those same removed files:

   • Line 78: Follow scripts/audit-prep-checklist.py
   • Line 152: Follow references/regulatory-inspection-guide.md
   • Line 153: Follow references/certification-audit-guide.md
   • Line 154: Follow references/customer-audit-guide.md

   An agent following these instructions will try to read files that no longer exist (or are no longer documented as available). Either restore those reference files, replace the Follow ... directives with inline prose guidance, or remove these stale references.

_{Last reviewed commit: "Remove redundant saf..."}